Is scaling to absolute zero a bad way to hide an element?
In my opinion, you are fine to use zero for a scaling factor for objects - those scaled meshes will simply be reduced down to a point, but with no actual loss of geometry; increasing the scale factor again will restore your mesh and while scaled down to a point will not be visible in your render.

However, for scaling faces, you will lose geometry by scaling down to zero in Edit mode - since all vertices will exist at the exact same point so there is nothing to 'scale back up'. Note though, that in this situation, even scaling down to a very small scale (but not zero) may introduce rounding issues with the vertices in your mesh when you scale back up again. The exception to this is if you are scaling the faces using a modifier (such as an Armature or Deform modifier) since the underlying geometry is not actually affected and so can be restored without distortion.